Add parameter docs to README and CI/CD workflow

[ypriverol]

Summary

• Modernized README.md with full parameter reference tables, quick start examples, and build instructions
• Created GitHub Actions CI/CD workflow (included below — requires workflow token scope to push)

README Changes

• Full parameter reference tables covering all 30+ command-line flags, organized by category:
  • Core search (tolerance, isotope error, TDA)
  • Fragmentation and instrument settings
  • Enzyme and digestion options
  • Peptide filtering (length, charge, MS level)
  • Modifications and protocol
  • Output and performance tuning
  • Advanced parameters
• Quick start examples for basic and TMT searches
• Modification file format documentation with examples
• Build-from-source instructions
• Updated requirements to Java 17+

CI/CD Workflow

The GitHub token lacks workflow scope, so the CI file needs to be added manually. Create .github/workflows/ci.yml:

name: CI

on:
  push:
    branches: [ master, dev ]
  pull_request:
    branches: [ master, dev ]

jobs:
  build:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        java: [ '17', '21' ]

    steps:
      - uses: actions/checkout@v4

      - name: Set up JDK ${{ matrix.java }}
        uses: actions/setup-java@v4
        with:
          java-version: ${{ matrix.java }}
          distribution: 'temurin'
          cache: 'maven'

      - name: Build with Maven
        run: mvn compile -q

      - name: Run tests
        run: mvn test

      - name: Package JAR
        run: mvn package -DskipTests -q

      - name: Upload JAR artifact
        if: matrix.java == '17'
        uses: actions/upload-artifact@v4
        with:
          name: MSGFPlus-jar
          path: target/MSGFPlus.jar
          retention-days: 30

Test plan

• mvn compile — clean compilation
• mvn test — 137 tests run, 0 failures, 0 errors
• README renders correctly with parameter tables

🤖 Generated with Claude Code

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feature/ci-readme-cleanup

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